Fri May 7 10:53:25 UTC 2021 I: starting to build qtltools/buster/armhf on jenkins on '2021-05-07 10:53' Fri May 7 10:53:25 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_33/2883/console.log Fri May 7 10:53:25 UTC 2021 I: Downloading source for buster/qtltools=1.1+dfsg-3 --2021-05-07 10:53:25-- http://deb.debian.org/debian/pool/main/q/qtltools/qtltools_1.1+dfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2196 (2.1K) Saving to: ‘qtltools_1.1+dfsg-3.dsc’ 0K .. 100% 254M=0s 2021-05-07 10:53:25 (254 MB/s) - ‘qtltools_1.1+dfsg-3.dsc’ saved [2196/2196] Fri May 7 10:53:25 UTC 2021 I: qtltools_1.1+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: qtltools Binary: qtltools, qtltools-example Architecture: any all Version: 1.1+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://qtltools.github.io/qtltools/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/qtltools Vcs-Git: https://salsa.debian.org/med-team/qtltools.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libblas-dev, libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libeigen3-dev, libgsl-dev, libhts-dev, r-mathlib, zlib1g-dev Package-List: qtltools deb science optional arch=any qtltools-example deb doc optional arch=all Checksums-Sha1: 167eeb9ee4b7d51169a4d8ccb898d217d3a8f90a 91192 qtltools_1.1+dfsg.orig.tar.xz dcf821835f96d4283fda52ce192bcf3e8a8d432e 13556112 qtltools_1.1+dfsg-3.debian.tar.xz Checksums-Sha256: 2bfb7a838e11399bad01a4415ab2a9810f39cc4eb37e0e569e03beac37f0a902 91192 qtltools_1.1+dfsg.orig.tar.xz c644bcc108ff88f7a86a3fb20ae781f7454047a2d8a56233ab1bd85a12401d0e 13556112 qtltools_1.1+dfsg-3.debian.tar.xz Files: f221d7205dbe8d824b5eea2a37a11fc6 91192 qtltools_1.1+dfsg.orig.tar.xz b4be6c08ce8aa656199315904f9a05bb 13556112 qtltools_1.1+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluagEsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEZig//UOYhIfrSjKWafMkb9WuybGuz5H6mFArU bvyFLnyb4YmmTUbX4Y+fRiR+vDZMpcxLcx/r1LluF7KEeMBLVS4zGc017I0+/86k gYR06DKdfV+56jSIUg9ZJqlC6H0dZ+dGlOe6umx6d6VlTn247DhbPsuF3mVGrsB+ P5TqwWO/Z+ib7jmtILQm8oj1TZN5hmMn+y+Obn/U1+sA24E8uAuHQUc1D1oH1Kde eX2P1Y3fdtGF++iU6NnqmmyAAJKciheweGPPYeaNo+C2B5KNTlxkQcz/F57jAPe9 h97wq7YNoo/3XJEnGcdhLOeW2Nw4dbVI9mFQA8mN/XJrk4HUmAWsbrWeUQKZwD00 nmS2/oBjmRK+TuQ7XkohKM1GN1jKmuuV9tmuPnQEIVIFoWpi9yTjrX2iLg/jwaLi +Cfb3Fy67mA5/PhZM7G4HZweD4dYKtYMhRAmpTUO/0QblTL5D+aFpZMvRBX9v3TB D0kx8Ozu+rSfFBYxHFN4EV1M6eLzw2klg6oE7G/MhPp3yIvOCZKcOkU4NdA3B5hL eHKnnNVB2p+Evuagx+ds0H9bmO90UDmlfrPeJ/i5RB087ynbC/Ui2nUjr1BdfE/S r1q76EZwmrWmtIgTmooYuFPGiYYZjxGuO50qI+0qSWVmZtfcRR6xJW+4L1bUp+5K 4QJj2Hx3kko= =9fFy -----END PGP SIGNATURE----- Fri May 7 10:53:25 UTC 2021 I: Checking whether the package is not for us Fri May 7 10:53:25 UTC 2021 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Fri May 7 10:53:25 UTC 2021 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Fri May 7 12:57:58 UTC 2021 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 6 22:53:50 -12 2021 I: pbuilder-time-stamp: 1620384830 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [qtltools_1.1+dfsg-3.dsc] I: copying [./qtltools_1.1+dfsg.orig.tar.xz] I: copying [./qtltools_1.1+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 13 03:20:43 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./qtltools_1.1+dfsg-3.dsc dpkg-source: info: extracting qtltools in qtltools-1.1+dfsg dpkg-source: info: unpacking qtltools_1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking qtltools_1.1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile_config.patch dpkg-source: info: applying Spelling_error.patch dpkg-source: info: applying reproducible_build.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17693/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='c5838fe08ce44a78a26aee0775096816' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='17693' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/pbuilderrc_AZ9W --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/b1 --logfile b1/build.log qtltools_1.1+dfsg-3.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux virt64a 5.10.0-6-arm64 #1 SMP Debian 5.10.28-1 (2021-04-09) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 May 6 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/17693/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), libblas-dev, libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libeigen3-dev, libgsl-dev, libhts-dev, r-mathlib, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on r-mathlib; however: Package r-mathlib is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost1.67-dev{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libeigen3-dev{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu-dev{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} r-mathlib{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix r-base-core r-base-dev shared-mime-info wget xdg-user-dirs 0 packages upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 50.6 MB of archives. After unpacking 280 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2+deb10u1 [104 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3+deb10u1 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u2 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u2 [65.6 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+deb10u1 [597 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main armhf icu-devtools armhf 63.1-6+deb10u1 [168 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libblas-dev armhf 3.8.0-2 [117 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libboost-regex1.67.0 armhf 1.67.0-13+deb10u1 [438 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libicu-dev armhf 63.1-6+deb10u1 [8940 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libboost-regex1.67-dev armhf 1.67.0-13+deb10u1 [538 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libboost-iostreams1.67-dev armhf 1.67.0-13+deb10u1 [254 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libboost-iostreams-dev armhf 1.67.0.1 [3632 B] Get: 44 http://deb.debian.org/debian buster/main armhf libboost-program-options1.67.0 armhf 1.67.0-13+deb10u1 [336 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libboost-program-options1.67-dev armhf 1.67.0-13+deb10u1 [385 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libboost-program-options-dev armhf 1.67.0.1 [3656 B] Get: 47 http://deb.debian.org/debian buster/main armhf libbz2-dev armhf 1.0.6-9.2~deb10u1 [28.8 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3+deb10u1 [62.3 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3+deb10u1 [119 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u5 [1299 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3+deb10u1 [323 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3+deb10u1 [137 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u6 [202 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 60 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u1 [295 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB] Get: 64 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libeigen3-dev all 3.3.7-1 [850 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.1 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libgsl23 armhf 2.5+dfsg-6 [718 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libgsl-dev armhf 2.5+dfsg-6 [903 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB] Get: 70 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get: 71 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 73 http://deb.debian.org/debian buster/main armhf r-mathlib armhf 3.5.2-1 [1811 kB] Fetched 50.6 MB in 7s (6818 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. 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Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../27-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... 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Unpacking libboost-regex1.67.0:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:armhf. Preparing to unpack .../39-libicu-dev_63.1-6+deb10u1_armhf.deb ... Unpacking libicu-dev:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libboost-regex1.67-dev:armhf. Preparing to unpack .../40-libboost-regex1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-regex1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:armhf. Preparing to unpack .../41-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-iostreams1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:armhf. Preparing to unpack .../42-libboost-iostreams-dev_1.67.0.1_armhf.deb ... Unpacking libboost-iostreams-dev:armhf (1.67.0.1) ... Selecting previously unselected package libboost-program-options1.67.0:armhf. Preparing to unpack .../43-libboost-program-options1.67.0_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-program-options1.67.0:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options1.67-dev:armhf. Preparing to unpack .../44-libboost-program-options1.67-dev_1.67.0-13+deb10u1_armhf.deb ... Unpacking libboost-program-options1.67-dev:armhf (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options-dev:armhf. Preparing to unpack .../45-libboost-program-options-dev_1.67.0.1_armhf.deb ... Unpacking libboost-program-options-dev:armhf (1.67.0.1) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../46-libbz2-dev_1.0.6-9.2~deb10u1_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../47-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../48-libkrb5support0_1.17-3+deb10u1_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3+deb10u1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../49-libk5crypto3_1.17-3+deb10u1_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3+deb10u1) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../50-libssl1.1_1.1.1d-0+deb10u5_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u5) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../51-libkrb5-3_1.17-3+deb10u1_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../52-libgssapi-krb5-2_1.17-3+deb10u1_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3+deb10u1) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../53-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../54-libsasl2-2_2.1.27+dfsg-1+deb10u1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../55-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../56-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../57-libnghttp2-14_1.36.0-2+deb10u1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../58-libpsl5_0.20.2-2_armhf.deb ... Unpacking libpsl5:armhf (0.20.2-2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../59-librtmp1_2.4+20151223.gitfa8646d.1-2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../60-libssh2-1_1.8.0-2.1_armhf.deb ... Unpacking libssh2-1:armhf (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../61-libcurl3-gnutls_7.64.0-4+deb10u1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../62-libdeflate0_1.2-1_armhf.deb ... Unpacking libdeflate0:armhf (1.2-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../63-pkg-config_0.29-6_armhf.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../64-libeigen3-dev_3.3.7-1_all.deb ... Unpacking libeigen3-dev (3.3.7-1) ... Selecting previously unselected package libgslcblas0:armhf. Preparing to unpack .../65-libgslcblas0_2.5+dfsg-6_armhf.deb ... Unpacking libgslcblas0:armhf (2.5+dfsg-6) ... Selecting previously unselected package libgsl23:armhf. Preparing to unpack .../66-libgsl23_2.5+dfsg-6_armhf.deb ... Unpacking libgsl23:armhf (2.5+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../67-libgsl-dev_2.5+dfsg-6_armhf.deb ... Unpacking libgsl-dev (2.5+dfsg-6) ... Selecting previously unselected package libhts2:armhf. Preparing to unpack .../68-libhts2_1.9-11_armhf.deb ... Unpacking libhts2:armhf (1.9-11) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../69-liblzma-dev_5.2.4-1_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../70-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../71-libhts-dev_1.9-11_armhf.deb ... Unpacking libhts-dev:armhf (1.9-11) ... Selecting previously unselected package r-mathlib. Preparing to unpack .../72-r-mathlib_3.5.2-1_armhf.deb ... Unpacking r-mathlib (3.5.2-1) ... Setting up libboost1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libboost-program-options1.67.0:armhf (1.67.0-13+deb10u1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up libpsl5:armhf (0.20.2-2) ... Setting up libgslcblas0:armhf (2.5+dfsg-6) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libboost-program-options1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:armhf (1.1.1d-0+deb10u5) ... Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u2) ... Setting up libdeflate0:armhf (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3+deb10u1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libboost-program-options-dev:armhf (1.67.0.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:armhf (2.5+dfsg-6) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up icu-devtools (63.1-6+deb10u1) ... Setting up pkg-config (0.29-6) ... Setting up libk5crypto3:armhf (1.17-3+deb10u1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:armhf (8.3.0-6) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up r-mathlib (3.5.2-1) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up libkrb5-3:armhf (1.17-3+deb10u1) ... Setting up libbsd0:armhf (0.9.1-2+deb10u1) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libicu-dev:armhf (63.1-6+deb10u1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+deb10u1) ... Setting up libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libboost-regex1.67.0:armhf (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-regex1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libblas3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libeigen3-dev (3.3.7-1) ... Setting up libgssapi-krb5-2:armhf (1.17-3+deb10u1) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libboost-iostreams1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libblas-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Setting up libboost-iostreams-dev:armhf (1.67.0.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libhts2:armhf (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:armhf (1.9-11) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/qtltools-1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../qtltools_1.1+dfsg-3_source.changes dpkg-buildpackage: info: source package qtltools dpkg-buildpackage: info: source version 1.1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/qtltools-1.1+dfsg' rm -f debian/upstream.example/examples.tar.xz dh_auto_clean make -j3 clean make[2]: Entering directory '/build/qtltools-1.1+dfsg' rm -f obj/*.o bin/QTLtools make[2]: Leaving directory '/build/qtltools-1.1+dfsg' make[1]: Leaving directory '/build/qtltools-1.1+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/qtltools-1.1+dfsg' mkdir -p /build/qtltools-1.1+dfsg/obj/ mkdir -p /build/qtltools-1.1+dfsg/bin/ dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/qtltools-1.1+dfsg' g++ -std=c++0x -o obj/QTLtools.o -c src/QTLtools.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/data.o -c src/common/data.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_main.o -c src/mode_ase/ase_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_genotypes.o -c src/mode_ase/ase_read_genotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_sequences.o -c src/mode_ase/ase_read_sequences.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_main.o -c src/mode_bamstat/bamstat_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_ase/ase_read_genotypes.cpp: In member function 'void ase_data::readGenotypes(std::__cxx11::string, std::__cxx11::string)': src/mode_ase/ase_read_genotypes.cpp:42:27: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("Not compressed with bgzip"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_ase/ase_read_genotypes.cpp:43:3: note: here case idx_load_failed: vrb.error("Impossible to load index file"); ^~~~ src/mode_ase/ase_read_genotypes.cpp:43:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_ase/ase_read_genotypes.cpp:44:3: note: here case file_type_error: vrb.error("Unrecognized file format"); ^~~~ src/mode_ase/ase_read_genotypes.cpp:44:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("Unrecognized file format"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_ase/ase_read_genotypes.cpp:45:3: note: here default: vrb.error("Unknown error when opening"); ^~~~~~~ g++ -std=c++0x -o obj/bamstat_read_annotations.o -c src/mode_bamstat/bamstat_read_annotations.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_read_bam.o -c src/mode_bamstat/bamstat_read_bam.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_write_output.o -c src/mode_bamstat/bamstat_write_output.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_chunking.o -c src/mode_cis/cis_chunking.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_collapse_phenotypes.o -c src/mode_cis/cis_collapse_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_conditionnal_pass.o -c src/mode_cis/cis_conditionnal_pass.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_cis/cis_conditionnal_pass.cpp:16: src/mode_cis/cis_data.h: In member function 'double cis_data::getCorrelation(std::vector&, std::vector&)': src/mode_cis/cis_data.h:148:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_cis/cis_data.h:149:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_cis/cis_data.h:149:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_cis/cis_data.h:150:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:31, from src/mode_cis/cis_collapse_phenotypes.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/cis_initilization.o -c src/mode_cis/cis_initilization.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:31, from src/mode_cis/cis_conditionnal_pass.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void cis_data::runConditionalPass(std::__cxx11::string)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/cis_learn_beta.o -c src/mode_cis/cis_learn_beta.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_learn_dof.o -c src/mode_cis/cis_learn_dof.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_main.o -c src/mode_cis/cis_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_management.o -c src/mode_cis/cis_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_nominal_pass.o -c src/mode_cis/cis_nominal_pass.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_cis/cis_nominal_pass.cpp:16: src/mode_cis/cis_data.h: In member function 'double cis_data::getCorrelation(std::vector&, std::vector&)': src/mode_cis/cis_data.h:148:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_cis/cis_data.h:149:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_cis/cis_data.h:149:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_cis/cis_data.h:150:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ g++ -std=c++0x -o obj/cis_permutation_pass.o -c src/mode_cis/cis_permutation_pass.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_covariates.o -c src/mode_cis/cis_read_covariates.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_genotypes.o -c src/mode_cis/cis_read_genotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_cis/cis_permutation_pass.cpp:16: src/mode_cis/cis_data.h: In member function 'double cis_data::getCorrelation(std::vector&, std::vector&)': src/mode_cis/cis_data.h:148:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_cis/cis_data.h:149:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_cis/cis_data.h:149:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_cis/cis_data.h:150:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ g++ -std=c++0x -o obj/cis_read_phenotypes.o -c src/mode_cis/cis_read_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_thresholds.o -c src/mode_cis/cis_read_thresholds.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_main.o -c src/mode_correct/correct_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_management.o -c src/mode_correct/correct_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_processing.o -c src/mode_correct/correct_processing.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_read_covariates.o -c src/mode_correct/correct_read_covariates.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_correct/correct_read_covariates.cpp: In member function 'void correct_data::readQTLCovariates(std::__cxx11::string, std::__cxx11::string)': src/mode_correct/correct_read_covariates.cpp:92:59: warning: unused variable 'nsl' [-Wunused-variable] int ngt, ngt_arr = 0, nds, nds_arr = 0, * gt_arr = NULL, nsl, nsl_arr = 0, * sl_arr = NULL; ^~~ src/mode_correct/correct_read_covariates.cpp:92:64: warning: unused variable 'nsl_arr' [-Wunused-variable] int ngt, ngt_arr = 0, nds, nds_arr = 0, * gt_arr = NULL, nsl, nsl_arr = 0, * sl_arr = NULL; ^~~~~~~ src/mode_correct/correct_read_covariates.cpp:92:79: warning: unused variable 'sl_arr' [-Wunused-variable] int ngt, ngt_arr = 0, nds, nds_arr = 0, * gt_arr = NULL, nsl, nsl_arr = 0, * sl_arr = NULL; ^~~~~~ g++ -std=c++0x -o obj/extract_main.o -c src/mode_extract/extract_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/extract_managment.o -c src/mode_extract/extract_managment.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/extract_read_data.o -c src/mode_extract/extract_read_data.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/extract_write.o -c src/mode_extract/extract_write.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_extract/extract_read_data.cpp: In member function 'void extract_data::readVCF(std::__cxx11::string)': src/mode_extract/extract_read_data.cpp:101:27: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_extract/extract_read_data.cpp:102:3: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_extract/extract_read_data.cpp:102:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_extract/extract_read_data.cpp:103:3: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_extract/extract_read_data.cpp:103:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_extract/extract_read_data.cpp:104:3: note: here default : vrb.error("Unknown error!"); ^~~~~~~ g++ -std=c++0x -o obj/fdensity_main.o -c src/mode_fdensity/fdensity_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fdensity_process.o -c src/mode_fdensity/fdensity_process.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fdensity_read_annotation.o -c src/mode_fdensity/fdensity_read_annotation.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fdensity_read_qtl.o -c src/mode_fdensity/fdensity_read_qtl.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_main.o -c src/mode_fenrich/fenrich_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_management.o -c src/mode_fenrich/fenrich_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_process.o -c src/mode_fenrich/fenrich_process.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_read_annotation.o -c src/mode_fenrich/fenrich_read_annotation.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_read_qtl.o -c src/mode_fenrich/fenrich_read_qtl.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_read_tss.o -c src/mode_fenrich/fenrich_read_tss.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_binning_process.o -c src/mode_genrich/genrich_binning_process.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_main.o -c src/mode_genrich/genrich_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_process.o -c src/mode_genrich/genrich_process.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_auxillliary_data.o -c src/mode_genrich/genrich_read_auxillliary_data.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_phenotypes.o -c src/mode_genrich/genrich_read_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_reference_genotypes.o -c src/mode_genrich/genrich_read_reference_genotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_routines.o -c src/mode_genrich/genrich_routines.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_genrich/genrich_read_reference_genotypes.cpp: In member function 'void genrich_data::readReferenceGenotypes(std::__cxx11::string)': src/mode_genrich/genrich_read_reference_genotypes.cpp:26:27: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_genrich/genrich_read_reference_genotypes.cpp:27:3: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_genrich/genrich_read_reference_genotypes.cpp:27:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_genrich/genrich_read_reference_genotypes.cpp:28:3: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_genrich/genrich_read_reference_genotypes.cpp:28:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_genrich/genrich_read_reference_genotypes.cpp:29:3: note: here default : vrb.error("Unknown error!"); ^~~~~~~ g++ -std=c++0x -o obj/match_main.o -c src/mode_match/match_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_managment.o -c src/mode_match/match_managment.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_process.o -c src/mode_match/match_process.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_read_genotypes.o -c src/mode_match/match_read_genotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_read_sequences.o -c src/mode_match/match_read_sequences.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_main.o -c src/mode_pca/pca_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_match/match_read_genotypes.cpp: In member function 'void match_data::readGenotypes(std::__cxx11::string, std::__cxx11::string)': src/mode_match/match_read_genotypes.cpp:40:27: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("Not compressed with bgzip"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_match/match_read_genotypes.cpp:41:3: note: here case idx_load_failed: vrb.error("Impossible to load index file"); ^~~~ src/mode_match/match_read_genotypes.cpp:41:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_match/match_read_genotypes.cpp:42:3: note: here case file_type_error: vrb.error("Unrecognized file format"); ^~~~ src/mode_match/match_read_genotypes.cpp:42:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("Unrecognized file format"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_match/match_read_genotypes.cpp:43:3: note: here default: vrb.error("Unknown error when opening"); ^~~~~~~ g++ -std=c++0x -o obj/pca_management.o -c src/mode_pca/pca_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_pca.o -c src/mode_pca/pca_pca.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_read_data.o -c src/mode_pca/pca_read_data.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_chunking.o -c src/mode_quan/quan_chunking.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_pca/pca_read_data.cpp: In member function 'void pca_data::readDataVCF(std::__cxx11::string)': src/mode_pca/pca_read_data.cpp:47:37: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_pca/pca_read_data.cpp:48:13: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_pca/pca_read_data.cpp:48:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_pca/pca_read_data.cpp:49:13: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_pca/pca_read_data.cpp:49:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_pca/pca_read_data.cpp:50:13: note: here default : vrb.error("Unknown error!"); ^~~~~~~ g++ -std=c++0x -o obj/quan_main.o -c src/mode_quan/quan_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_management.o -c src/mode_quan/quan_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_printResults.o -c src/mode_quan/quan_printResults.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_readBAM.o -c src/mode_quan/quan_readBAM.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_readGTF.o -c src/mode_quan/quan_readGTF.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_chunking.o -c src/mode_rtc/rtc_chunking.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_collapse_phenotypes.o -c src/mode_rtc/rtc_collapse_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_common.o -c src/mode_rtc/rtc_common.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_gwas_cis.o -c src/mode_rtc/rtc_gwas_cis.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_rtc/rtc_common.cpp:16: src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector&, std::vector&, int)': src/mode_rtc/rtc_data.h:300:22: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_rtc/rtc_data.h:301:9: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_rtc/rtc_data.h:301:22: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_rtc/rtc_data.h:302:9: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector&, std::vector&)': src/mode_rtc/rtc_data.h:276:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_rtc/rtc_data.h:277:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_rtc/rtc_data.h:277:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_rtc/rtc_data.h:278:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_collapse_phenotypes.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pairsToTestForRTC&}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from lib/OTools/otools.h:29, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/queue:62, from lib/OTools/otools.h:22, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from lib/OTools/otools.h:29, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In member function 'void rtc_data::calculateRTC(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from lib/OTools/otools.h:29, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_gwas_cis.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_gwas_trans.o -c src/mode_rtc/rtc_gwas_trans.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_initilization.o -c src/mode_rtc/rtc_initilization.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_main.o -c src/mode_rtc/rtc_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_gwas_trans.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_management.o -c src/mode_rtc/rtc_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_mergeQTL_cis.o -c src/mode_rtc/rtc_mergeQTL_cis.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_mergeQTL_trans.o -c src/mode_rtc/rtc_mergeQTL_trans.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_rtc/rtc_management.cpp:16: src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector&, std::vector&)': src/mode_rtc/rtc_data.h:276:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_rtc/rtc_data.h:277:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_rtc/rtc_data.h:277:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_rtc/rtc_data.h:278:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_mergeQTL_cis.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_read_covariates.o -c src/mode_rtc/rtc_read_covariates.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_read_genotypes.o -c src/mode_rtc/rtc_read_genotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_mergeQTL_trans.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pairsToTestForRTC}; _Tp = pairsToTestForRTC; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_read_get_hotspots.o -c src/mode_rtc/rtc_read_get_hotspots.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_rtc/rtc_read_genotypes.cpp: In member function 'void rtc_data::readGenotypesVCF(std::__cxx11::string)': src/mode_rtc/rtc_read_genotypes.cpp:81:27: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:82:3: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_rtc/rtc_read_genotypes.cpp:82:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:83:3: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_rtc/rtc_read_genotypes.cpp:83:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:84:3: note: here default : vrb.error("Unknown error!"); ^~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp: In member function 'int rtc_data::readGenotypesVCFStats(std::__cxx11::string, std::__cxx11::string&, std::vector >&)': src/mode_rtc/rtc_read_genotypes.cpp:263:37: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:264:13: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_rtc/rtc_read_genotypes.cpp:264:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:265:13: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_rtc/rtc_read_genotypes.cpp:265:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:266:13: note: here default : vrb.error("Unknown error!"); ^~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp: In member function 'void rtc_data::scanGenotypesVCF(std::__cxx11::string)': src/mode_rtc/rtc_read_genotypes.cpp:330:37: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:331:13: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_rtc/rtc_read_genotypes.cpp:331:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:332:13: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_rtc/rtc_read_genotypes.cpp:332:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_rtc/rtc_read_genotypes.cpp:333:13: note: here default : vrb.error("Unknown error!"); ^~~~~~~ g++ -std=c++0x -o obj/rtc_read_phenotypes.o -c src/mode_rtc/rtc_read_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_sampling.o -c src/mode_rtc/rtc_sampling.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_adjust.o -c src/mode_trans/trans_adjust.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_rtc/rtc_sampling.cpp:16: src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector&, std::vector&, int)': src/mode_rtc/rtc_data.h:300:22: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_rtc/rtc_data.h:301:9: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_rtc/rtc_data.h:301:22: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_rtc/rtc_data.h:302:9: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector&, std::vector&)': src/mode_rtc/rtc_data.h:276:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_rtc/rtc_data.h:277:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_rtc/rtc_data.h:277:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_rtc/rtc_data.h:278:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ g++ -std=c++0x -o obj/trans_analysis_pass.o -c src/mode_trans/trans_analysis_pass.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/c++/8/set:60, from lib/OTools/otools.h:25, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_sampling.cpp:16: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from lib/OTools/otools.h:26, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_sampling.cpp:16: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/algorithm:62, from lib/OTools/otools.h:29, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_sampling.cpp:16: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/queue:62, from lib/OTools/otools.h:22, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_sampling.cpp:16: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from lib/OTools/otools.h:29, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_sampling.cpp:16: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'rtc_sample_results rtc_data::sampleRTC(std::vector&, std::vector&, int, double, int)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/trans_chunking.o -c src/mode_trans/trans_chunking.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_trans/../common/data.h:19, from src/mode_trans/trans_data.h:26, from src/mode_trans/trans_adjust.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void trans_data::buildNullDistribution(std::__cxx11::string)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/trans_initilization.o -c src/mode_trans/trans_initilization.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_trans/trans_analysis_pass.cpp:16: src/mode_trans/trans_data.h: In member function 'double trans_data::fastCorrelation(std::vector&, float*)': src/mode_trans/trans_data.h:122:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += P[i+2] * G[i+2]; ~~~~~^~~~~~~~~~~~~~~~~~ src/mode_trans/trans_data.h:123:2: note: here case 2: sum0 += P[i+1] * G[i+1]; ^~~~ src/mode_trans/trans_data.h:123:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += P[i+1] * G[i+1]; ~~~~~^~~~~~~~~~~~~~~~~~ src/mode_trans/trans_data.h:124:2: note: here case 1: sum0 += P[i+0] * G[i+0]; ^~~~ g++ -std=c++0x -o obj/trans_learn_beta.o -c src/mode_trans/trans_learn_beta.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_main.o -c src/mode_trans/trans_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_managment.o -c src/mode_trans/trans_managment.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_covariates.o -c src/mode_trans/trans_read_covariates.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_phenotypes.o -c src/mode_trans/trans_read_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_samples.o -c src/mode_trans/trans_read_samples.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_initilization.o -c src/mode_union/union_initilization.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_main.o -c src/mode_union/union_main.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_management.o -c src/mode_union/union_management.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_covariates.o -c src/mode_union/union_read_covariates.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_genotypes.o -c src/mode_union/union_read_genotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_get_hotspots.o -c src/mode_union/union_read_get_hotspots.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_union/union_read_genotypes.cpp: In member function 'void union_data::readGenotypesVCF(std::__cxx11::string, std::__cxx11::string)': src/mode_union/union_read_genotypes.cpp:76:27: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_union/union_read_genotypes.cpp:77:3: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_union/union_read_genotypes.cpp:77:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_union/union_read_genotypes.cpp:78:3: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_union/union_read_genotypes.cpp:78:34: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_union/union_read_genotypes.cpp:79:3: note: here default : vrb.error("Unknown error!"); ^~~~~~~ src/mode_union/union_read_genotypes.cpp: In member function 'void union_data::scanGenotypesVCF(std::__cxx11::string)': src/mode_union/union_read_genotypes.cpp:248:37: warning: this statement may fall through [-Wimplicit-fallthrough=] case not_bgzf: vrb.error("File not compressed with bgzip!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_union/union_read_genotypes.cpp:249:13: note: here case idx_load_failed: vrb.error("Impossible to load index file!"); ^~~~ src/mode_union/union_read_genotypes.cpp:249:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case idx_load_failed: vrb.error("Impossible to load index file!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_union/union_read_genotypes.cpp:250:13: note: here case file_type_error: vrb.error("File format not detected by htslib!"); ^~~~ src/mode_union/union_read_genotypes.cpp:250:44: warning: this statement may fall through [-Wimplicit-fallthrough=] case file_type_error: vrb.error("File format not detected by htslib!"); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/mode_union/union_read_genotypes.cpp:251:13: note: here default : vrb.error("Unknown error!"); ^~~~~~~ g++ -std=c++0x -o obj/union_read_phenotypes.o -c src/mode_union/union_read_phenotypes.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_union.o -c src/mode_union/union_union.cpp -O2 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/qtltools-1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from src/mode_union/union_union.cpp:16: src/mode_union/union_data.h: In member function 'double union_data::getCorrelation(std::vector&, std::vector&)': src/mode_union/union_data.h:189:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: sum0 += vec1[i+2] * vec2[i+2]; src/mode_union/union_data.h:190:2: note: here case 2: sum0 += vec1[i+1] * vec2[i+1]; ^~~~ src/mode_union/union_data.h:190:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: sum0 += vec1[i+1] * vec2[i+1]; src/mode_union/union_data.h:191:2: note: here case 1: sum0 += vec1[i+0] * vec2[i+0]; ^~~~ In file included from /usr/include/c++/8/vector:69, from lib/OTools/otools.h:20, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, from src/mode_union/union_union.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from lib/OTools/otools.h:20, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, from src/mode_union/union_union.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In member function 'void union_data::find_unions(std::vector >&, std::vector >&, std::vector >&, std::vector >&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -std=c++0x obj/QTLtools.o obj/data.o obj/ase_main.o obj/ase_read_genotypes.o obj/ase_read_sequences.o obj/bamstat_main.o obj/bamstat_read_annotations.o obj/bamstat_read_bam.o obj/bamstat_write_output.o obj/cis_chunking.o obj/cis_collapse_phenotypes.o obj/cis_conditionnal_pass.o obj/cis_initilization.o obj/cis_learn_beta.o obj/cis_learn_dof.o obj/cis_main.o obj/cis_management.o obj/cis_nominal_pass.o obj/cis_permutation_pass.o obj/cis_read_covariates.o obj/cis_read_genotypes.o obj/cis_read_phenotypes.o obj/cis_read_thresholds.o obj/correct_main.o obj/correct_management.o obj/correct_processing.o obj/correct_read_covariates.o obj/extract_main.o obj/extract_managment.o obj/extract_read_data.o obj/extract_write.o obj/fdensity_main.o obj/fdensity_process.o obj/fdensity_read_annotation.o obj/fdensity_read_qtl.o obj/fenrich_main.o obj/fenrich_management.o obj/fenrich_process.o obj/fenrich_read_annotation.o obj/fenrich_read_qtl.o obj/fenrich_read_tss.o obj/genrich_binning_process.o obj/genrich_main.o obj/genrich_process.o obj/genrich_read_auxillliary_data.o obj/genrich_read_phenotypes.o obj/genrich_read_reference_genotypes.o obj/genrich_routines.o obj/match_main.o obj/match_managment.o obj/match_process.o obj/match_read_genotypes.o obj/match_read_sequences.o obj/pca_main.o obj/pca_management.o obj/pca_pca.o obj/pca_read_data.o obj/quan_chunking.o obj/quan_main.o obj/quan_management.o obj/quan_printResults.o obj/quan_readBAM.o obj/quan_readGTF.o obj/rtc_chunking.o obj/rtc_collapse_phenotypes.o obj/rtc_common.o obj/rtc_gwas_cis.o obj/rtc_gwas_trans.o obj/rtc_initilization.o obj/rtc_main.o obj/rtc_management.o obj/rtc_mergeQTL_cis.o obj/rtc_mergeQTL_trans.o obj/rtc_read_covariates.o obj/rtc_read_genotypes.o obj/rtc_read_get_hotspots.o obj/rtc_read_phenotypes.o obj/rtc_sampling.o obj/trans_adjust.o obj/trans_analysis_pass.o obj/trans_chunking.o obj/trans_initilization.o obj/trans_learn_beta.o obj/trans_main.o obj/trans_managment.o obj/trans_read_covariates.o obj/trans_read_phenotypes.o obj/trans_read_samples.o obj/union_initilization.o obj/union_main.o obj/union_management.o obj/union_read_covariates.o obj/union_read_genotypes.o obj/union_read_get_hotspots.o obj/union_read_phenotypes.o obj/union_union.o -lRmath -lhts -lboost_iostreams -lboost_program_options -o bin/QTLtools -lz -lgsl -lblas -lbz2 -lm -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/qtltools-1.1+dfsg' make[1]: Leaving directory '/build/qtltools-1.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/qtltools-1.1+dfsg' cd debian/upstream.example && find -type f | LC_ALL=C sort | tar -T - --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner -Jcvf examples.tar.xz ./genes.50percent.chr22.bed.gz ./genes.50percent.chr22.bed.gz.tbi ./genes.covariates.pc50.txt.gz ./genes.simulated.chr22.bed.gz ./genes.simulated.chr22.bed.gz.tbi ./genotypes.chr22.vcf.gz ./genotypes.chr22.vcf.gz.tbi dh_install make[1]: Leaving directory '/build/qtltools-1.1+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/qtltools/usr/bin/QTLtools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/qtltools/usr/bin/QTLtools was not linked against libz.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/qtltools/usr/bin/QTLtools was not linked against libbz2.so.1.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/qtltools/usr/bin/QTLtools was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'qtltools-dbgsym' in '../qtltools-dbgsym_1.1+dfsg-3_armhf.deb'. dpkg-deb: building package 'qtltools' in '../qtltools_1.1+dfsg-3_armhf.deb'. dpkg-deb: building package 'qtltools-example' in '../qtltools-example_1.1+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../qtltools_1.1+dfsg-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/17693 and its subdirectories I: Current time: Fri May 7 00:47:21 -12 2021 I: pbuilder-time-stamp: 1620391641 Fri May 7 12:58:01 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ff2a-armhf-rb.debian.net. Fri May 7 12:58:01 UTC 2021 I: Preparing to do remote build '2' on ff2a-armhf-rb.debian.net. Fri May 7 19:18:43 UTC 2021 I: Deleting $TMPDIR on ff2a-armhf-rb.debian.net. Fri May 7 19:18:48 UTC 2021 I: qtltools_1.1+dfsg-3_armhf.changes: Format: 1.8 Date: Thu, 13 Sep 2018 16:07:01 +0200 Source: qtltools Binary: qtltools qtltools-dbgsym qtltools-example Architecture: armhf all Version: 1.1+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: qtltools - Tool set for molecular QTL discovery and analysis qtltools-example - Tool set for molecular QTL discovery and analysis - example Changes: qtltools (1.1+dfsg-3) unstable; urgency=medium . * Team upload. . [ Dylan Aïssi ] * Fix registries ref. * Update metadata references. * Canonical Vcs-Browser. * Bump Standards-Version to 4.1.1 (no changes needed). . [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: f3abcff04957f88b31ac44c3fa3eec72ef5ab6a8 162822544 qtltools-dbgsym_1.1+dfsg-3_armhf.deb 80501b0215f1f6128a966f6e4f3014ee439dcd2a 13556672 qtltools-example_1.1+dfsg-3_all.deb f12c41c465aa91a42dc0259614ececa806cdca9a 6503 qtltools_1.1+dfsg-3_armhf.buildinfo e3edc09ef978ec76f79dd654bf96b269e64df901 542740 qtltools_1.1+dfsg-3_armhf.deb Checksums-Sha256: b928b7026373f5a4757e60386f5a1936b9321c8db1407aa8d26d14b5ec160de4 162822544 qtltools-dbgsym_1.1+dfsg-3_armhf.deb ee187b50e8b009b738258faa809c93be76f2de2a08c7491b26b9f248070ce131 13556672 qtltools-example_1.1+dfsg-3_all.deb 521fde8b3f05e37d8a45128d5d6bda37e74e9e2d09b727f012c7298e0d446eb5 6503 qtltools_1.1+dfsg-3_armhf.buildinfo 15013964f77a8091491cf969eea82d3319cda67bb787236998d8275a70a5a5c0 542740 qtltools_1.1+dfsg-3_armhf.deb Files: e5fc842c445974933c7c5dd0cdeedee7 162822544 debug optional qtltools-dbgsym_1.1+dfsg-3_armhf.deb b769660346a40f5f71c10ea168c3e31b 13556672 doc optional qtltools-example_1.1+dfsg-3_all.deb 9437233a622d1f428d80f355fad2f4f8 6503 science optional qtltools_1.1+dfsg-3_armhf.buildinfo 8c7e43bf7d7ae70df557c102951dc1d8 542740 science optional qtltools_1.1+dfsg-3_armhf.deb Fri May 7 19:18:52 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/qtltools_1.1+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/qtltools_1.1+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/qtltools_1.1+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/b1/qtltools_1.1+dfsg-3_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.lq1CIGLjGA/b2/qtltools_1.1+dfsg-3_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 15.797s) 15.797s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 12.423s) 12.423s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri May 7 19:19:11 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Fri May 7 19:19:11 UTC 2021 I: qtltools from buster built successfully and reproducibly on armhf. Fri May 7 19:19:14 UTC 2021 I: Submitting .buildinfo files to external archives: Fri May 7 19:19:14 UTC 2021 I: Submitting 8.0K b1/qtltools_1.1+dfsg-3_armhf.buildinfo.asc Fri May 7 19:19:16 UTC 2021 I: Submitting 8.0K b2/qtltools_1.1+dfsg-3_armhf.buildinfo.asc Fri May 7 19:19:17 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 7 19:19:17 UTC 2021 I: Done submitting .buildinfo files. Fri May 7 19:19:17 UTC 2021 I: Removing signed qtltools_1.1+dfsg-3_armhf.buildinfo.asc files: removed './b1/qtltools_1.1+dfsg-3_armhf.buildinfo.asc' removed './b2/qtltools_1.1+dfsg-3_armhf.buildinfo.asc'